Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean.
Identifieur interne : 000712 ( Main/Exploration ); précédent : 000711; suivant : 000713Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean.
Auteurs : Chao Zhong [République populaire de Chine] ; Suli Sun [République populaire de Chine] ; Yinping Li [République populaire de Chine] ; Canxing Duan [République populaire de Chine] ; Zhendong Zhu [République populaire de Chine]Source :
- TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik [ 1432-2242 ] ; 2018.
Descripteurs français
- KwdFr :
- Cartographie chromosomique (MeSH), Gènes de plante (MeSH), Locus de caractère quantitatif (MeSH), Maladies des plantes (génétique), Maladies des plantes (microbiologie), Marqueurs génétiques (MeSH), Mutation de type INDEL (MeSH), Phytophthora (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (MeSH), Répétitions microsatellites (MeSH), Résistance à la maladie (génétique), Soja (génétique), Soja (microbiologie), Séquence nucléotidique (MeSH), Séquençage nucléotidique à haut débit (MeSH).
- MESH :
- génétique : Maladies des plantes, Résistance à la maladie, Soja.
- microbiologie : Maladies des plantes, Soja.
- Cartographie chromosomique, Gènes de plante, Locus de caractère quantitatif, Marqueurs génétiques, Mutation de type INDEL, Phytophthora, Phénotype, Polymorphisme de nucléotide simple, Répétitions microsatellites, Séquence nucléotidique, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Chromosome Mapping (MeSH), Disease Resistance (genetics), Genes, Plant (MeSH), Genetic Markers (MeSH), High-Throughput Nucleotide Sequencing (MeSH), INDEL Mutation (MeSH), Microsatellite Repeats (MeSH), Phenotype (MeSH), Phytophthora (MeSH), Plant Diseases (genetics), Plant Diseases (microbiology), Polymorphism, Single Nucleotide (MeSH), Quantitative Trait Loci (MeSH), Soybeans (genetics), Soybeans (microbiology).
- MESH :
- chemical : Genetic Markers.
- genetics : Disease Resistance, Plant Diseases, Soybeans.
- microbiology : Plant Diseases, Soybeans.
- Base Sequence, Chromosome Mapping, Genes, Plant, High-Throughput Nucleotide Sequencing, INDEL Mutation, Microsatellite Repeats, Phenotype, Phytophthora, Polymorphism, Single Nucleotide, Quantitative Trait Loci.
Abstract
KEY MESSAGE
A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F
DOI: 10.1007/s00122-017-3016-z
PubMed: 29138903
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Suli" sort="Sun, Suli" uniqKey="Sun S" first="Suli" last="Sun">Suli Sun</name><affiliation wicri:level="1"><nlm:affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Li, Yinping" sort="Li, Yinping" uniqKey="Li Y" first="Yinping" last="Li">Yinping Li</name><affiliation wicri:level="1"><nlm:affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Duan, Canxing" sort="Duan, Canxing" uniqKey="Duan C" first="Canxing" last="Duan">Canxing Duan</name><affiliation wicri:level="1"><nlm:affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Zhu, Zhendong" sort="Zhu, Zhendong" uniqKey="Zhu Z" first="Zhendong" last="Zhu">Zhendong Zhu</name><affiliation wicri:level="1"><nlm:affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhuzhendong@caas.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author></analytic><series><title level="j">TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</title><idno type="eISSN">1432-2242</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Chromosome Mapping (MeSH)</term><term>Disease Resistance (genetics)</term><term>Genes, Plant (MeSH)</term><term>Genetic Markers (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>INDEL Mutation (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Phenotype (MeSH)</term><term>Phytophthora (MeSH)</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (microbiology)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Quantitative Trait Loci (MeSH)</term><term>Soybeans (genetics)</term><term>Soybeans (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie chromosomique (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (microbiologie)</term><term>Marqueurs génétiques (MeSH)</term><term>Mutation de type INDEL (MeSH)</term><term>Phytophthora (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Répétitions microsatellites (MeSH)</term><term>Résistance à la maladie (génétique)</term><term>Soja (génétique)</term><term>Soja (microbiologie)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Disease Resistance</term><term>Plant Diseases</term><term>Soybeans</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Maladies des plantes</term><term>Résistance à la maladie</term><term>Soja</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Soja</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Soybeans</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Chromosome Mapping</term><term>Genes, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>INDEL Mutation</term><term>Microsatellite Repeats</term><term>Phenotype</term><term>Phytophthora</term><term>Polymorphism, Single Nucleotide</term><term>Quantitative Trait Loci</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Gènes de plante</term><term>Locus de caractère quantitatif</term><term>Marqueurs génétiques</term><term>Mutation de type INDEL</term><term>Phytophthora</term><term>Phénotype</term><term>Polymorphisme de nucléotide simple</term><term>Répétitions microsatellites</term><term>Séquence nucléotidique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>KEY MESSAGE</b></p><p>A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29138903</PMID><DateCompleted><Year>2018</Year><Month>04</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-2242</ISSN><JournalIssue CitedMedium="Internet"><Volume>131</Volume><Issue>3</Issue><PubDate><Year>2018</Year><Month>Mar</Month></PubDate></JournalIssue><Title>TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</Title><ISOAbbreviation>Theor Appl Genet</ISOAbbreviation></Journal><ArticleTitle>Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean.</ArticleTitle><Pagination><MedlinePgn>525-538</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00122-017-3016-z</ELocationID><Abstract><AbstractText Label="KEY MESSAGE" NlmCategory="UNASSIGNED">A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F<sub>2:3</sub> population, was performed, and one 767-kb genomic region with ΔSNP-index ≥ 0.9 on chromosome 3 was identified as the RpsHC18 candidate region in Huachun 18. The candidate region was reduced to a 146-kb region by fine mapping. Nonsynonymous SNP and haplotype analyses were carried out in the 146-kb region among ten soybean genotypes using WGRS. Four specific nonsynonymous SNPs were identified in two nucleotide-binding sites-leucine-rich repeat (NBS-LRR) genes, RpsHC18-NBL1 and RpsHC18-NBL2, which were considered to be the candidate genes. Finally, one specific SNP marker in each candidate gene was successfully developed using a tetra-primer ARMS-PCR assay, and the two markers were verified to be specific for RpsHC18 and to effectively distinguish other known Rps genes. In this study, we applied an integrated genomic-based strategy combining WGRS with traditional genetic mapping to identify RpsHC18 candidate genes and develop diagnostic markers. These results suggest that next-generation sequencing is a precise, rapid and cost-effective way to identify candidate genes and develop diagnostic markers, and it can accelerate Rps gene cloning and marker-assisted selection for breeding of P. sojae-resistant soybean cultivars.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhong</LastName><ForeName>Chao</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Suli</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yinping</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duan</LastName><ForeName>Canxing</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Zhendong</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhuzhendong@caas.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>201303018</GrantID><Agency>Special Fund for Agroscientific Research in the Public Interest</Agency><Country></Country></Grant><Grant><GrantID>2016NWB036-12</GrantID><Agency>Program of Protection of Crop Germplasm Resources from the Ministry of Agriculture of the People's Republic of China</Agency><Country></Country></Grant><Grant><GrantID>NICGR2017-008</GrantID><Agency>the National Infrastructure for Crop Germplasm Resources</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>11</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Theor Appl Genet</MedlineTA><NlmUniqueID>0145600</NlmUniqueID><ISSNLinking>0040-5752</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060467" MajorTopicYN="N">Disease Resistance</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054643" MajorTopicYN="N">INDEL Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013025" MajorTopicYN="N">Soybeans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>07</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>11</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>4</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29138903</ArticleId><ArticleId 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first="Chao" last="Zhong">Chao Zhong</name></noRegion><name sortKey="Duan, Canxing" sort="Duan, Canxing" uniqKey="Duan C" first="Canxing" last="Duan">Canxing Duan</name><name sortKey="Li, Yinping" sort="Li, Yinping" uniqKey="Li Y" first="Yinping" last="Li">Yinping Li</name><name sortKey="Sun, Suli" sort="Sun, Suli" uniqKey="Sun S" first="Suli" last="Sun">Suli Sun</name><name sortKey="Zhu, Zhendong" sort="Zhu, Zhendong" uniqKey="Zhu Z" first="Zhendong" last="Zhu">Zhendong Zhu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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